CentC is a 156 bp centromeric satellite repeat.

• Collected 79 CentC repeats from NCBI.
• Abundance gives the relative size of the centromere from 360 Jiao lines using BWA.

CRM2 A Centromeric Retrotransposon of Maize 2.

• From UTE (Unique Transposable Element) files, mapped for abundance.
• Included for comparison against CentC abundance.

Genome Size Initial Genome Sizes were found simply by aligning maize reference cDNA to each Jiao line.

• Proved to be inaccurate as much of the cDNA is repetative.
• Lead to false positives in mapping.

Using parsesam.pl (Courtesy of Paul),

• a per-gene count of reads mapped was found.

Using Jeff's Perl one-liners to,

• find total number of reads
• % of reads mapping to each gene
• flag any gene that shows up more than 0.00001% (these will be ignored).
• skip 663 flagged genes from each abundance file.
• recalulate # of reads mapped.

• Before accounting for relative differences in Gsize.

Thanks guys.

• Kevin Distor, for sending me CRM UTEs
• Paul, for the parsesam.pl script
• Jeff, for answering all my questions and the Github guidance.